Contacts of the helix formed by residues 339 - 357 (chain B) in PDB entry 5J1T
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 339 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B TRP 3.9 0.6 + - - -
338B GLN* 1.3 73.7 - - - +
340B SER* 1.3 66.7 + - - +
341B ASP* 3.4 10.8 + - - +
342B THR* 2.8 42.4 + - - +
343B VAL* 3.1 21.5 + - - +
57C THR* 5.3 0.9 - - - +
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Residues in contact with SER 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338B GLN 3.2 3.2 + - - -
339B ASP* 1.3 74.8 + - - +
341B ASP* 1.3 62.6 + - - +
343B VAL 3.2 1.2 + - - -
344B LYS* 2.8 29.3 + - - +
371B PRO* 3.8 19.2 - - - +
373B GLY* 3.4 12.2 + - - -
374B SER* 2.9 33.4 + - - -
436B ASN* 5.2 3.4 + - - -
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Residues in contact with ASP 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A HIS* 4.9 2.5 + - - +
141A ALA* 4.2 16.8 - - - +
142A SER* 4.9 3.9 + - - -
339B ASP* 3.4 9.8 + - - +
340B SER* 1.3 82.7 + - - +
342B THR* 1.3 60.7 + - - +
344B LYS* 3.6 13.9 - - - +
345B LEU* 3.1 24.4 + - - +
436B ASN* 2.9 36.3 + - - +
57C THR* 4.2 24.2 + - + +
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Residues in contact with THR 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B GLN* 6.2 1.1 - - + -
339B ASP* 2.8 36.6 + - + +
341B ASP* 1.3 73.9 - - - +
343B VAL* 1.3 69.5 + - + +
345B LEU* 3.4 1.8 + - - -
346B LEU 3.1 9.9 + - - -
57C THR* 4.5 5.2 - - - +
58C THR* 3.3 27.4 + - - +
59C THR* 3.0 34.6 + - - +
60C TYR* 5.2 2.7 - - + +
65C GLN* 6.0 2.0 - - - +
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Residues in contact with VAL 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B ARG* 4.1 13.0 - - - +
338B GLN* 3.4 35.7 - - + +
339B ASP 3.1 16.0 + - - +
340B SER 3.8 3.4 - - - +
342B THR* 1.3 76.9 - - + +
344B LYS* 1.3 66.4 + - - +
346B LEU* 3.2 7.4 + - + +
347B VAL* 2.9 28.1 + - + +
370B PHE* 3.7 32.5 - - + -
371B PRO* 4.0 13.5 - - + -
374B SER* 3.9 9.2 - - - +
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Residues in contact with LYS 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A PRO* 2.8 30.5 + - - +
140A HIS* 3.9 12.5 - - + +
141A ALA 5.3 0.6 - - - +
340B SER* 2.8 17.7 + - - +
341B ASP* 3.6 16.2 - - - +
342B THR 3.3 0.2 - - - -
343B VAL* 1.3 76.4 - - - +
345B LEU* 1.4 56.1 + - - +
347B VAL* 3.5 4.1 + - - +
348B ASP* 3.0 30.7 + - - +
373B GLY 4.4 7.2 + - - +
374B SER* 3.7 25.2 - - - +
376B LEU* 4.4 19.0 - - - +
377B ILE* 3.9 33.9 - - + +
436B ASN* 4.0 17.4 + - - +
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Residues in contact with LEU 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A HIS* 3.6 25.0 - - + +
341B ASP 3.1 17.4 + - - +
342B THR* 3.7 4.9 - - - +
344B LYS* 1.4 75.0 - - - +
346B LEU* 1.3 64.9 + - - +
348B ASP* 3.4 1.9 + - - +
349B LEU* 3.0 47.3 + - + +
34C VAL* 4.2 12.3 - - + -
51C ALA* 4.2 10.1 - - + +
52C ILE 4.9 0.2 - - - -
53C THR* 3.9 24.0 - - + +
57C THR* 3.7 26.9 - - + +
58C THR 4.2 1.6 - - - -
59C THR* 3.7 27.6 - - + +
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Residues in contact with LEU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B ILE* 6.1 3.8 - - + -
335B ARG* 3.8 37.2 - - - +
342B THR 3.1 8.6 + - - +
343B VAL* 3.2 12.8 + - + +
345B LEU* 1.3 76.6 - - - +
347B VAL* 1.3 61.8 + - + +
349B LEU* 3.8 2.0 - - - +
350B GLU* 2.9 56.6 + - + +
48C LEU* 4.1 17.0 - - + -
59C THR* 3.4 24.6 + - + +
60C TYR 4.1 20.9 - - - +
61C ALA* 4.9 3.4 - - - +
62C ASP* 4.5 2.7 - - - +
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Residues in contact with VAL 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ILE* 4.3 20.9 - - + -
335B ARG* 6.2 0.4 - - - +
343B VAL* 2.9 26.3 + - + +
344B LYS* 4.0 3.1 - - - +
346B LEU* 1.3 77.3 - - + +
348B ASP* 1.3 64.8 + - - +
350B GLU* 3.3 1.3 + - - +
351B LEU* 3.0 43.1 + - + +
370B PHE* 3.8 29.8 - - + -
374B SER* 5.7 1.6 - - - +
377B ILE* 3.8 22.9 - - + -
378B PHE* 3.9 15.3 - - + -
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Residues in contact with ASP 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A PRO* 4.7 1.6 - - - +
140A HIS* 2.7 29.5 + - - +
344B LYS 3.0 18.7 + - - +
345B LEU* 3.7 4.8 - - - +
346B LEU 3.3 0.2 - - - -
347B VAL* 1.3 77.0 - - - +
349B LEU* 1.3 62.3 + - + +
352B SER* 2.9 29.5 + - - -
377B ILE* 3.8 19.0 - - + +
380B LYS* 2.8 25.8 + - - +
381B TYR* 2.7 40.1 + - - -
99C ARG* 6.3 0.4 - - - -
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Residues in contact with LEU 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B LEU* 3.0 38.4 + - + +
346B LEU 4.0 1.8 - - - +
348B ASP* 1.3 79.9 - - + +
350B GLU* 1.3 67.7 + - - +
352B SER* 4.6 1.8 - - - -
353B TYR* 3.0 28.9 + - - +
34C VAL* 4.1 14.4 - - + -
38C TYR* 4.8 7.2 + - - +
48C LEU* 4.2 20.6 - - + -
51C ALA* 3.4 33.9 - - + -
59C THR* 4.4 1.8 - - + -
99C ARG* 3.6 38.1 - - - +
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Residues in contact with GLU 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B ILE* 3.8 18.3 - - + +
329B GLN 5.7 2.8 - - - +
330B ILE* 4.0 22.2 - - + -
346B LEU* 2.9 42.8 + - + +
347B VAL 4.0 2.7 - - - +
349B LEU* 1.3 77.1 - - - +
351B LEU* 1.3 63.0 + - - +
353B TYR* 4.5 6.0 - - - +
354B GLY* 3.3 16.8 + - - -
48C LEU* 4.2 25.5 + - + +
61C ALA* 5.8 3.8 - - - +
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Residues in contact with LEU 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B ILE* 3.7 6.1 - - + +
330B ILE* 3.7 18.2 - - + -
347B VAL* 3.0 35.0 + - + +
350B GLU* 1.3 78.0 - - - +
352B SER* 1.3 63.8 + - - +
355B PHE* 2.9 40.8 + - + -
362B ALA* 3.5 31.4 - - + -
364B VAL* 4.9 2.5 - - + -
378B PHE* 4.2 15.3 - - + -
381B TYR* 3.7 41.1 - - + -
394B LEU* 4.3 6.3 - - + -
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Residues in contact with SER 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348B ASP* 2.9 24.3 + - - -
349B LEU* 4.4 1.6 - - - -
351B LEU* 1.3 73.8 - - - +
353B TYR* 1.3 57.9 + - - +
355B PHE* 3.8 0.3 - - - -
356B GLU* 2.6 56.7 + - - +
381B TYR* 3.4 11.8 + - - -
389B PHE* 3.8 8.5 - - - -
99C ARG* 3.2 14.5 + - - -
107C TYR* 2.7 25.6 + - - -
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Residues in contact with TYR 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B LEU 3.0 19.9 + - - +
350B GLU* 4.5 6.3 - - - +
352B SER* 1.3 78.0 - - - +
354B GLY* 1.3 67.1 + - - +
356B GLU* 3.7 11.4 + - - +
357B ASN* 2.9 63.4 + - + +
359B GLN* 5.8 1.3 - - - -
38C TYR* 3.8 37.0 - + + +
46C ARG* 3.6 42.0 - - - +
47C GLU* 5.7 0.2 - - - -
48C LEU 6.1 0.2 - - - -
97C ASN* 5.9 0.2 - - - -
99C ARG* 4.5 7.5 - - - +
113C TRP* 3.8 25.1 - + - -
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Residues in contact with GLY 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B ILE* 3.6 16.6 - - - -
350B GLU 3.3 10.7 + - - -
353B TYR* 1.3 84.4 - - - +
355B PHE* 1.3 62.3 + - - +
357B ASN* 3.2 9.7 + - - -
358B GLY 3.4 0.5 + - - -
359B GLN* 3.0 43.8 + - - +
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Residues in contact with PHE 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B ILE* 3.6 14.6 - - + -
351B LEU* 2.9 39.5 + - + +
354B GLY* 1.3 76.8 - - - +
356B GLU* 1.3 61.0 + - - +
357B ASN 3.4 0.5 + - - -
358B GLY* 3.7 6.9 + - - -
359B GLN 3.4 20.4 - - - +
361B ALA 3.9 17.0 - - - -
362B ALA* 4.0 21.8 - - + -
381B TYR* 4.3 11.4 - + - -
389B PHE* 3.6 45.6 - + + -
392B VAL* 3.6 39.0 - - + -
393B ALA 4.3 3.1 - - - -
394B LEU* 4.4 6.3 - - + -
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Residues in contact with GLU 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B SER* 2.6 45.1 + - - +
353B TYR* 3.7 10.1 - - - +
354B GLY 3.3 0.2 - - - -
355B PHE* 1.3 76.3 - - - +
357B ASN* 1.3 68.8 + - - +
358B GLY 3.5 1.4 + - - -
389B PHE* 3.8 15.0 - - + -
99C ARG* 3.0 21.5 + - - -
107C TYR* 4.0 2.3 + - - -
109C THR* 2.9 30.2 + - - +
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Residues in contact with ASN 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B TYR* 2.9 64.1 + - + +
354B GLY* 3.2 3.5 + - - +
356B GLU* 1.3 91.2 + - - +
358B GLY* 1.3 58.2 + - - +
359B GLN* 3.5 6.1 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il